6pv5 - Revision history

OCA at 07:36, 11 October 2023

OCA — Wed, 11 Oct 2023 07:36:30 GMT

←Older revision		Revision as of 07:36, 11 October 2023
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	<StructureSection load='6pv5' size='340' side='right'caption='[[6pv5]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='6pv5' size='340' side='right'caption='[[6pv5]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pv5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Clop1 Clop1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PV5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens_ATCC_13124 Clostridium perfringens ATCC 13124]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PV5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.18Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6pv4\|6pv4]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CPF_0875 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=195103 CLOP1])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6pv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pv5 OCA], [https://pdbe.org/6pv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pv5 RCSB], [https://www.ebi.ac.uk/pdbsum/6pv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pv5 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6pv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pv5 OCA], [~~http~~://pdbe.org/6pv5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pv5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pv5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pv5 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H2YTZ1_CLOP1 A0A0H2YTZ1_CLOP1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clop1~~]]	+	[[Category: Clostridium perfringens ATCC 13124]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Boraston AB]]
-	[[Category: Pluvinage, B]]	+	[[Category: Pluvinage B]]
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 17:52, 20 November 2019

OCA — Wed, 20 Nov 2019 17:52:09 GMT

←Older revision		Revision as of 17:52, 20 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6pv5 is ~~ON HOLD until Paper~~ Publication	+	==Structure of CpGH84B==
		+	<StructureSection load='6pv5' size='340' side='right'caption='[[6pv5]], [[Resolution\|resolution]] 2.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6pv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clop1 Clop1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PV5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pv4\|6pv4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPF_0875 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=195103 CLOP1])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6pv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pv5 OCA], [http://pdbe.org/6pv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pv5 RCSB], [http://www.ebi.ac.uk/pdbsum/6pv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pv5 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The opportunistic pathogen Clostridium perfringens possesses the ability to colonize the protective mucin layer in the gastrointestinal tract. To assist this, the C. perfringens genome contains a battery of genes encoding glycoside hydrolases (GHs) that are likely active on mucin glycans, including four genes encoding family 84 GHs: CpGH84A (NagH), CpGH84B (NagI), CpGH84C (NagJ) and CpGH84D (NagK). To probe the potential advantage gained by the expansion of GH84 enzymes in C. perfringens, we undertook the structural and functional characterization of the CpGH84 catalytic modules. Here, we show that these four CpGH84 catalytic modules act as beta-N-acetyl-D-glucosaminidases able to hydrolyze N- and O-glycan motifs. CpGH84A and CpGH84D displayed a substrate specificity restricted to terminal beta-1,2- and beta-1,6-linked N-acetyl-D-glucosamine (GlcNAc). CpGH84B and CpGH84C appear more promiscuous with activity on terminal beta-1,2-, beta-1,3- and beta-1,6-linked GlcNAc; both possess some activity toward beta-1,4-linked GlcNAc, but this is dependent upon which monosaccharide it is linked to. Furthermore, all the CpGH84s have different optimum pHs ranging from 5.2 to 7.0. Consistent with their beta-N-acetyl-D-glucosaminidase activities, the structures of the four catalytic modules revealed similar folds with a catalytic site including a conserved -1 subsite that binds GlcNAc. However, nonconserved residues in the vicinity of the +1 subsite suggest different accommodation of the sugar preceding the terminal GlcNAc, resulting in subtly different substrate specificities. This structure-function comparison of the four GH84 catalytic modules from C. perfringens reveals their different biochemical properties, which may relate to how they are deployed in the bacterium's niche in the host.

-	~~Authors: Pluvinage~~, B., ~~Boraston~~, A.B.	+	Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens.,Pluvinage B, Massel PM, Burak K, Boraston AB Glycobiology. 2019 Sep 6. pii: 5561588. doi: 10.1093/glycob/cwz069. PMID:31701135<ref>PMID:31701135</ref>

-	~~Description: Structure~~ of ~~CpGH84B~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Boraston, A.B]]	+	<div class="pdbe-citations 6pv5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Clop1]]
		+	[[Category: Large Structures]]
		+	[[Category: Boraston, A B]]
	[[Category: Pluvinage, B]]		[[Category: Pluvinage, B]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "6pv5" [edit=sysop:move=sysop]

OCA — Wed, 31 Jul 2019 04:45:32 GMT

Protected "6pv5" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:45, 31 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pv5 is ON HOLD until Paper Publication Authors: Pluvinage, B., Boraston, A.B. Description: Structure of CpGH84B [[Category: Unreleased Structures]...

OCA — Wed, 31 Jul 2019 04:45:30 GMT

New page: '''Unreleased structure''' The entry 6pv5 is ON HOLD until Paper Publication Authors: Pluvinage, B., Boraston, A.B. Description: Structure of CpGH84B [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 6pv5 is ON HOLD until Paper Publication

Authors: Pluvinage, B., Boraston, A.B.

Description: Structure of CpGH84B
[[Category: Unreleased Structures]]
[[Category: Boraston, A.B]]
[[Category: Pluvinage, B]]